Adeloye-Fave/afriomics

Free, open-source multi-omics pipeline (metagenomics · metatranscriptomics · metabolomics) for African microbiome research — with disease modelling, cross-body-site interaction networks, and African reference context. No-code GUI + Snakemake + Jupyter. 100% free tools. # AfriOmics 🌍 ## Free, Open-Source Multi-Omics Microbiome Pipeline for African Research --- ## What is AfriOmics? AfriOmics is a complete, free, Africa-contextualised multi-omics microbiome pipeline integrating: | Module | Omics Layer | Biological Question | |--------|-------------|---------------------| | 🧬 Metagenomics | Shotgun DNA sequencing | **Who is there?** (species composition) | | 🔬 Metatranscriptomics | RNA sequencing | **What are they actively doing?** | | ⚗️ Metabolomics | LC-MS/MS mass spectrometry | **What are they producing?** | | 🔗 Integration | MOFA+ · DIABLO · Networks | **How do they interact?** | | 🦠 Disease Modelling | Random Forest · ROC | **What predicts disease?** | Results are benchmarked against curated African reference microbiome datasets (AWI-Gen, H3Africa) across six body sites, and linked to endemic African infectious disease models (malaria, HIV, TB, schistosomiasis). --- ## Quick Start ### Option A — No-Code GUI (Easiest) ```bash # Install R and Shiny Rscript -e "install.packages(c('shiny','bslib','ggplot2','dplyr','vegan','plotly','DT'))" # Launch the GUI Rscript -e "shiny::runApp('shiny/')" # Open localhost in your browser # Upload your MetaPhlAn4 profile and metadata → click Run Analysis ``` ### Option B — Jupyter Notebooks (Step-by-step) ```bash # Install dependencies pip install pandas numpy matplotlib seaborn plotly scipy scikit-learn networkx pyvis # Open notebooks in order: jupyter notebook notebooks/01_metagenomics_walkthrough.ipynb jupyter notebook notebooks/02_metatranscriptomics_walkthrough.ipynb jupyter notebook notebooks/03_metabolomics_walkthrough.ipynb jupyter notebook notebooks/04_integration_disease_modelling.ipynb ``` ### Option C — Full Snakemake Pipeline (Advanced) ```bash # Clone repository git clone github.com cd afriomics # Install conda environments (one-time setup, ~30 min) conda env create -f envs/environments.yaml # Edit config nano config/config_co …